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pmid:34538870
Integrated Bioinformatic Analysis of Competing Endogenous RNA Network of Choriocarcinoma.
Qianxia Tan · Zhihui Tan · Junliang Liu · Yanqun Mo · Huining Liu
Medical science monitor : international medical journal of experimental and clinical research · 2021 doi:10.12659/MSM.931475
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Complete file
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The competing endogenous RNA (ceRNA) network plays an important role in the occurrence and development of carcinoma. However, the involvement of the ceRNA network in CC remains unclear. The current study aimed to investigate the regulatory mechanism of ceRNA in CC. MATERIAL AND METHODS We downloaded the messenger RNAs (mRNAs) expression profiles (GSE20510 and GSE65654) and microRNAs (miRNAs) expression profiles (GSE32346 and GSE130489) from GEO datasets. The limma package of R software was used to identify differentially expressed RNAs (DERNAs). Then, we performed functional annotation of the differentially expressed mRNAs (DEmRNAs). TargetScan, miRDB, miRWalk, and Starbase were used to construct a CC-specific ceRNA network and select key molecules. RESULTS The results identified a total of 177 DEmRNAs and 189 differentially expressed miRNAs (DEmiRNAs) between the trophoblast and CC cell line samples. Ten differentially expressed lncRNAs (DElncRNAs) were obtained based on experimental studies. The DEmRNAs were mainly enriched in cell proliferation, positive regulation of the apoptotic process, and cell death. A total of 10 genes were ascertained as hub genes. Based on DEmRNAs, DEmiRNAs, and DElncRNAs, a CC-specific ceRNA network was established. Five DElncRNAs, 15 DEmiRNAs, and 45 DEmRNAs were identified. In addition, LINC00261, MEG3, MALAT1, H19, and OGFRP1 were identified as 5 key lncRNAs in choriocarcinoma. 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P value"], ["MAGT4A", "3.2192", "1.23E-08", "1.43E-07"], ["MXRA8", "3.5007", "3.55E-08", "3.07E-07"], ["APOA2", "2.6460", "4.83E-10", "2.12E-08"], ["CCR7", "2.4503", "2.63E-05", "7.39E-05"], ["ACKR3", "1.9622", "7.69E-07", "3.63E-06"], ["GPC4", "2.8810", "5.55E-06", "1.94E-05"], ["MAGEA12", "5.3826", "1.69E-15", "8.25E-12"], ["MAGEA1", "2.2676", "5.76E-10", "2.24E-08"], ["MAGEA6", "5.8546", "2.66E-15", "8.25E-12"], ["FSTL1", "−6.1075", "5.19E-15", "1.24E-11"], ["IGFBP3", "−2.8418", "1.79E-09", "4.10E-08"], ["IGFBP7", "−2.3101", "2.83E-09", "5.32E-08"], ["CYR61", "−2.3364", "6.88E-06", "2.32E-05"], ["FBN1", "−2.8740", "5.25E-11", "7.41E-09"], ["CKAP4", "−1.5676", "0.001285", "0.002333"], ["NMU", "−2.1097", "4.14E-06", "1.50E-05"], ["GNAI2", "−2.3328", "1.01E-07", "6.85E-07"], ["GNG11", "−3.0939", "1.22E-13", "1.46E-10"], ["WNT5A", "−1.9255", "2.87E-06", "1.10E-05"], ["DKK1", "−3.5953", "2.28E-08", "2.19E-07"], ["JUN", "−1.8796", "4.73E-08", "3.84E-07"], ["CTGF", "−5.4197", "8.13E-12", "2.17E-09"], ["SRGN", "−4.0831", "1.46E-11", "3.15E-09"], ["BGN", "−1.7001", "1.02E-07", "6.88E-07"]], "row_count": 25, "column_count": 4, "numeric_cells": 75, "header_rows": 1, "locator": "section[14]/table-wrap[1]#t2-medscimonit-27-e931475"}}, {"id": "asset:table:pmid:34538870:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e54d5a43c1957254b6e0a9668ac2463840b82e5b7290beb9f527c2d9b4aec030", "bytes": 1049, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#t3-medscimonit-27-e931475", "version": null, "note": "DEmiRNAs interact with the DEmRNAs retrieved from miRDB, TargetScan and miRWalk database.", "structure": {"pmcid": "PMC8462126", "section_index": 15, "section_title": "CC-Specific ceRNA Network", "row_count": 16, "column_count": 2}, "table": {"label": "Table 3", "caption": "DEmiRNAs interact with the DEmRNAs retrieved from miRDB, TargetScan and miRWalk database.", "rows": [["miRNAs", "mRNAs"], ["has-miR-10b", "CTPS2"], ["has-miR-155", "DLX6, NR6A1, ANKRD6, TCF4, BDNF"], ["has-miR-598", "LIN28A, ID1, LBH"], ["has-miR-411", "PHKB, ACVR2B, MGAT4A"], ["has-miR-370", "NR6A1, RAB3B"], ["has-miR-134", "NR6A1, ACVR2B, FAT2, RFTN1, BDNF"], ["has-miR-539", "NR3C1, SERPINE2, DA2AP2, NR6A1, ICK, RAB3B, DNMT3B, WNT5A, FAM111A, NFIB"], ["has-miR-10a", "BDNF"], ["has-miR-376c", "NFIB, ATP10D"], ["has-miR-495", "ACVR2B, TCF4, SLC26A2"], ["has-miR-152", "TXNIP, CTPS2, ATP10D, NR3C1, CCNG1, MET, ELMO1, ATP2B4, DDAH1, TXNIP, ALCAM, TCF4, FBN1, MGAT4A"], ["has-miR-372", "TXNIP, EPHA2, RAB3B, NFIB, ANKRD6, TFPI2, MGAT4A, THAP10, MAGEA6, ALDH1A3"], ["has-miR-520f", "ASAP2, WNT5A, ATP10D, GNAI2, RND3, CCKBR, TSPAN12, NFIB"], ["has-miR-934", "RAB3B"], ["has-miR-1270", "ATP10D, NR3C1, TPD52L1, CCR7"]], "row_count": 16, "column_count": 2, "numeric_cells": 23, "header_rows": 1, "locator": "section[15]/table-wrap[1]#t3-medscimonit-27-e931475"}}, {"id": "asset:table:pmid:34538870:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7323ee2cb1174e322af552e39a4e946b51c82266fded07ca9b10b74dd7520f71", "bytes": 1588, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[1]#t4-medscimonit-27-e931475", "version": null, "note": "The list of DEmRNAs, including 82 upregulated DEmRNAs and 95 downregulated DEmRNAs.", "structure": {"pmcid": "PMC8462126", "section_index": 18, "section_title": "Supplementary Data", "row_count": 3, "column_count": 2}, "table": {"label": "Supplementary Table 1", "caption": "The list of DEmRNAs, including 82 upregulated DEmRNAs and 95 downregulated DEmRNAs.", "rows": [["Regulation", "mRNAs"], ["Upregulated (n=82)", "C1orf106, PTN, NDUFAF4, AKR1B10, RGS16, YBX2, MXRA8, ANKRD6, JADE3, F2RL1, SLC2A3, SH2B2, DENND1A, DNMT3B, FYB, FAT2, CTSV, SARS, CLDN6, AGTPBP1, SNX10, ATP1A1, DLX6, ACTR6, CRYBA2, BNIP3, APOA2, IMPA2, CTH, NR6A1, SFN, CCKBR, TPD52L1, TYRO3, REEP1, CCR7, EPCAM, ZNF215, ICK, RFK, COL9A3, GPC4, SLC39A4, DNMT3L, TSPAN12, IRX4, KHDC1L, NLRP2, FZD5, HAND1, DDX3Y, CCNG1, ELOVL6, KHDRBS3, FBLN2, MAGEA6, TMEM38B, ELMO1, MYCN, ZNF415, LHFP, ATP2B4, NMRK2, C1orf105, MGAT4A, MAGEA1, CYB5R2, ACVR2B, CRIP1, ADAM8, SLC29A2, GATA2, MAGEA12, PCSK5, CBLC, LIN28A, HMGA1, TFF1, ZNF280A, PHKB, ACKR3, ANKZF1"], ["Downregulated (n=95)", "FSTL1, CD44, FAM111A, HSPB1, BID, BTBD3, ID3, MET, MARCKS, AXL, MSN, GNAI2, SERPINE2, PAPSS2, BMPR1A, ATP9A, EPHA2, SEL1L3, TRAF5, THAP10, NFIB, PLP2, RFTN1, DAZAP2, TSPO, RAB3B, BDNF, DDAH1, MEIS2, ZNF175, ALCAM, ID1, EMP3, ARMCX1, DPYD, IGFBP7, VASH1, SLC26A2, TCF4, GNG11, DKK1, ADORA2B, NR3C1, IL7R, IFI16, OXCT1, ASAP2, CAP2, ALDH1A3, SH3BGRL3, MEST, KLF2, SGK1, COL5A2, VIM, FAT1, GSTO1, HLA-A, RHOBTB3, ATP10D, NYNRIN, C11orf95, FRZB, CTPS2, WNT5A, NMU, INPP1, NT5E, SCCPDH, IGFBP3, RND3, SRGN, PMP22, CDR2L, TMSB4X, S100A6, TFPI2, JUN, GLCE, MT2A, FBN1, LBH, TGFBI, HOXB2, BGN, CYR61, TXNIP, ZAK, CTGF, ECI2, ZNF22, UCP2, EFEMP1, CKAP4, CBR1"]], "row_count": 3, "column_count": 2, "numeric_cells": 4, "header_rows": 1, "locator": "section[18]/table-wrap[1]#t4-medscimonit-27-e931475"}}, {"id": "asset:table:pmid:34538870:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c3dae7f0292187672681ad171d2c284eae1a1bbf960db94046983490acf7873b", "bytes": 3012, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[18]/table-wrap[2]#t5-medscimonit-27-e931475", "version": null, "note": "The list of DEmiRNAs, including 128 upregulated DEmiRNAs and 60 downregulated DEmiRNAs.", "structure": {"pmcid": "PMC8462126", "section_index": 18, "section_title": "Supplementary Data", "row_count": 3, "column_count": 2}, "table": {"label": "Supplementary Table 2", "caption": "The list of DEmiRNAs, including 128 upregulated DEmiRNAs and 60 downregulated DEmiRNAs.", "rows": [["Regulation", "miRNAs"], ["Upregulated (n=128)", "hsa-miR-376b, hsa-miR-146a, hsa-miR-147, hsa-miR-642, hsa-miR-873, hsa-miR-380, hsa-miR-125b, hsa-miR-542-3p, hsa-miR-886-5p, hsa-miR-138, hsa-miR-127-3p, hsa-miR-654-3p, hsa-miR-126, hsa-let-7d, hsa-miR-29a, hsa-miR-488, hsa-miR-192, hsa-let-7g, hsa-miR-124, hsa-miR-133a, hsa-miR-616, has-miR-155, hsa-miR-222, hsa-miR-432, hsa-miR-184, hsa-miR-125a-5p, hsa-miR-125a-3p, hsa-miR-487a, hsa-miR-337-5p, hsa-miR-221, hsa-miR-195, hsa-miR-487b, hsa-miR-28-3p, hsa-miR-198, hsa-miR-504, hsa-miR-214, hsa-miR-323-3p, hsa-miR-200a, hsa-miR-376c, hsa-miR-27a, hsa-miR-335, hsa-miR-152, hsa-miR-127-5p, hsa-miR-539, hsa-miR-496, hsa-miR-146b-5p, hsa-miR-99a, hsa-miR-133b, hsa-let-7b, hsa-miR-544, hsa-miR-143, hsa-miR-328, hsa-miR-139-5p, hsa-miR-320, hsa-let-7a, hsa-miR-889, hsa-miR-28-5p, hsa-miR-194, hsa-miR-628-5p, hsa-miR-217, hsa-miR-199b-5p, hsa-miR-342-5p, hsa-miR-493, hsa-miR-886-3p, hsa-miR-199a-3p, hsa-miR-134, hsa-miR-574-3p, hsa-miR-342-3p, hsa-miR-409-5p, hsa-miR-542-5p, hsa-miR-99b, hsa-let-7e, hsa-miR-370, hsa-miR-199a-5p, hsa-miR-758, hsa-miR-10b, hsa-miR-431, hsa-miR-216b, hsa-let-7c, hsa-miR-103, hsa-miR-129-3p, hsa-miR-24, hsa-miR-100, hsa-miR-379, hsa-miR-299-5p, hsa-miR-876-5p, hsa-miR-369-5p, hsa-miR-382, hsa-miR-654-5p, hsa-miR-186, hsa-miR-10a, hsa-miR-21, hsa-miR-598, hsa-miR-655, hsa-miR-302c, hsa-miR-137, hsa-miR-331-3p, hsa-miR-410, hsa-miR-329, hsa-miR-153, hsa-miR-494, hsa-miR-411, hsa-miR-485-3p, hsa-miR-324-3p, hsa-miR-876-3p, hsa-miR-376a, hsa-miR-363, hsa-miR-196b, hsa-miR-145, hsa-miR-874, hsa-miR-338-3p, hsa-miR-148b, hsa-miR-340, hsa-miR-140-3p, hsa-miR-147b, hsa-miR-497, hsa-miR-369-3p, hsa-let-7f, hsa-miR-218, hsa-miR-551b, hsa-miR-433, hsa-miR-154, hsa-miR-541, hsa-miR-142-3p, hsa-miR-495, hsa-miR-29c, hsa-miR-132, hsa-miR-29b"], ["Downregulated (n=60)", "hsa-miR-518d-5p, hsa-miR-520b, hsa-miR-520c-3p, hsa-miR-518e, hsa-miR-517b, hsa-miR-1276, hsa-miR-520g, hsa-miR-1301, hsa-miR-519b-3p, hsa-miR-1270, hsa-miR-769-3p, hsa-miR-512-3p, hsa-miR-483-3p, hsa-miR-519d, hsa-miR-1179, hsa-miR-520e, hsa-miR-93, hsa-miR-934, hsa-miR-523, hsa-let-7i, hsa-miR-1292, hsa-miR-520a-3p, hsa-miR-375, hsa-miR-31, hsa-miR-526b, hsa-miR-518c, hsa-miR-519c-3p, hsa-miR-29b-2, hsa-miR-18a, hsa-miR-769-5p, hsa-miR-516-3p, hsa-miR-92a-1, hsa-miR-519a, hsa-miR-519e, hsa-miR-520h, hsa-miR-522, hsa-miR-518f, hsa-miR-148a, hsa-miR-24-2, hsa-miR-524-5p, hsa-miR-29b-1, hsa-miR-516a-5p, hsa-miR-213, hsa-miR-520a-5p, hsa-miR-517, hsa-miR-641, hsa-miR-181a-2, hsa-miR-520f, hsa-miR-151-3p, hsa-miR-373, hsa-miR-944, hsa-miR-371-3p, hsa-miR-518b, hsa-miR-524, hsa-miR-517c, hsa-miR-372, hsa-miR-15b, hsa-miR-151-5P, hsa-miR-520d-5p, hsa-miR-744, hsa-miR-512-5p"]], "row_count": 3, "column_count": 2, "numeric_cells": 4, "header_rows": 1, "locator": "section[18]/table-wrap[2]#t5-medscimonit-27-e931475"}}, {"id": "asset:table:pmid:34538870:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:04a9d3a1db4688a06092174e8a5fd0b2c6be8b4e147027c58f1c174e1c1dab09", "bytes": 1587, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[23]/table-wrap[1]#db_ds_table-wrap1_reqid_", "version": null, "note": "The list of DEmRNAs, including 82 upregulated DEmRNAs and 95 downregulated DEmRNAs.", "structure": {"pmcid": "PMC8462126", "section_index": 23, "section_title": "Supplementary Materials", "row_count": 3, "column_count": 2}, "table": {"label": "Supplementary Table 1", "caption": "The list of DEmRNAs, including 82 upregulated DEmRNAs and 95 downregulated DEmRNAs.", "rows": [["Regulation", "mRNAs"], ["Upregulated (n=82)", "C1orf106, PTN, NDUFAF4, AKR1B10, RGS16, YBX2, MXRA8, ANKRD6, JADE3, F2RL1, SLC2A3, SH2B2, DENND1A, DNMT3B, FYB, FAT2, CTSV, SARS, CLDN6, AGTPBP1, SNX10, ATP1A1, DLX6, ACTR6, CRYBA2, BNIP3, APOA2, IMPA2, CTH, NR6A1, SFN, CCKBR, TPD52L1, TYRO3, REEP1, CCR7, EPCAM, ZNF215, ICK, RFK, COL9A3, GPC4, SLC39A4, DNMT3L, TSPAN12, IRX4, KHDC1L, NLRP2, FZD5, HAND1, DDX3Y, CCNG1, ELOVL6, KHDRBS3, FBLN2, MAGEA6, TMEM38B, ELMO1, MYCN, ZNF415, LHFP, ATP2B4, NMRK2, C1orf105, MGAT4A, MAGEA1, CYB5R2, ACVR2B, CRIP1, ADAM8, SLC29A2, GATA2, MAGEA12, PCSK5, CBLC, LIN28A, HMGA1, TFF1, ZNF280A, PHKB, ACKR3, ANKZF1"], ["Downregulated (n=95)", "FSTL1, CD44, FAM111A, HSPB1, BID, BTBD3, ID3, MET, MARCKS, AXL, MSN, GNAI2, SERPINE2, PAPSS2, BMPR1A, ATP9A, EPHA2, SEL1L3, TRAF5, THAP10, NFIB, PLP2, RFTN1, DAZAP2, TSPO, RAB3B, BDNF, DDAH1, MEIS2, ZNF175, ALCAM, ID1, EMP3, ARMCX1, DPYD, IGFBP7, VASH1, SLC26A2, TCF4, GNG11, DKK1, ADORA2B, NR3C1, IL7R, IFI16, OXCT1, ASAP2, CAP2, ALDH1A3, SH3BGRL3, MEST, KLF2, SGK1, COL5A2, VIM, FAT1, GSTO1, HLA-A, RHOBTB3, ATP10D, NYNRIN, C11orf95, FRZB, CTPS2, WNT5A, NMU, INPP1, NT5E, SCCPDH, IGFBP3, RND3, SRGN, PMP22, CDR2L, TMSB4X, S100A6, TFPI2, JUN, GLCE, MT2A, FBN1, LBH, TGFBI, HOXB2, BGN, CYR61, TXNIP, ZAK, CTGF, ECI2, ZNF22, UCP2, EFEMP1, CKAP4, CBR1"]], "row_count": 3, "column_count": 2, "numeric_cells": 4, "header_rows": 1, "locator": "section[23]/table-wrap[1]#db_ds_table-wrap1_reqid_"}}, {"id": "asset:table:pmid:34538870:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:5930566d7e27c6a56e808058dd15b824ba324294c2781640746daae4073a79eb", "bytes": 3011, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[23]/table-wrap[2]#db_ds_table-wrap2_reqid_", "version": null, "note": "The list of DEmiRNAs, including 128 upregulated DEmiRNAs and 60 downregulated DEmiRNAs.", "structure": {"pmcid": "PMC8462126", "section_index": 23, "section_title": "Supplementary Materials", "row_count": 3, "column_count": 2}, "table": {"label": "Supplementary Table 2", "caption": "The list of DEmiRNAs, including 128 upregulated DEmiRNAs and 60 downregulated DEmiRNAs.", "rows": [["Regulation", "miRNAs"], ["Upregulated (n=128)", "hsa-miR-376b, hsa-miR-146a, hsa-miR-147, hsa-miR-642, hsa-miR-873, hsa-miR-380, hsa-miR-125b, hsa-miR-542-3p, hsa-miR-886-5p, hsa-miR-138, hsa-miR-127-3p, hsa-miR-654-3p, hsa-miR-126, hsa-let-7d, hsa-miR-29a, hsa-miR-488, hsa-miR-192, hsa-let-7g, hsa-miR-124, hsa-miR-133a, hsa-miR-616, has-miR-155, hsa-miR-222, hsa-miR-432, hsa-miR-184, hsa-miR-125a-5p, hsa-miR-125a-3p, hsa-miR-487a, hsa-miR-337-5p, hsa-miR-221, hsa-miR-195, hsa-miR-487b, hsa-miR-28-3p, hsa-miR-198, hsa-miR-504, hsa-miR-214, hsa-miR-323-3p, hsa-miR-200a, hsa-miR-376c, hsa-miR-27a, hsa-miR-335, hsa-miR-152, hsa-miR-127-5p, hsa-miR-539, hsa-miR-496, hsa-miR-146b-5p, hsa-miR-99a, hsa-miR-133b, hsa-let-7b, hsa-miR-544, hsa-miR-143, hsa-miR-328, hsa-miR-139-5p, hsa-miR-320, hsa-let-7a, hsa-miR-889, hsa-miR-28-5p, hsa-miR-194, hsa-miR-628-5p, hsa-miR-217, hsa-miR-199b-5p, hsa-miR-342-5p, hsa-miR-493, hsa-miR-886-3p, hsa-miR-199a-3p, hsa-miR-134, hsa-miR-574-3p, hsa-miR-342-3p, hsa-miR-409-5p, hsa-miR-542-5p, hsa-miR-99b, hsa-let-7e, hsa-miR-370, hsa-miR-199a-5p, hsa-miR-758, hsa-miR-10b, hsa-miR-431, hsa-miR-216b, hsa-let-7c, hsa-miR-103, hsa-miR-129-3p, hsa-miR-24, hsa-miR-100, hsa-miR-379, hsa-miR-299-5p, hsa-miR-876-5p, hsa-miR-369-5p, hsa-miR-382, hsa-miR-654-5p, hsa-miR-186, hsa-miR-10a, hsa-miR-21, hsa-miR-598, hsa-miR-655, hsa-miR-302c, hsa-miR-137, hsa-miR-331-3p, hsa-miR-410, hsa-miR-329, hsa-miR-153, hsa-miR-494, hsa-miR-411, hsa-miR-485-3p, hsa-miR-324-3p, hsa-miR-876-3p, hsa-miR-376a, hsa-miR-363, hsa-miR-196b, hsa-miR-145, hsa-miR-874, hsa-miR-338-3p, hsa-miR-148b, hsa-miR-340, hsa-miR-140-3p, hsa-miR-147b, hsa-miR-497, hsa-miR-369-3p, hsa-let-7f, hsa-miR-218, hsa-miR-551b, hsa-miR-433, hsa-miR-154, hsa-miR-541, hsa-miR-142-3p, hsa-miR-495, hsa-miR-29c, hsa-miR-132, hsa-miR-29b"], ["Downregulated (n=60)", "hsa-miR-518d-5p, hsa-miR-520b, hsa-miR-520c-3p, hsa-miR-518e, hsa-miR-517b, hsa-miR-1276, hsa-miR-520g, hsa-miR-1301, hsa-miR-519b-3p, hsa-miR-1270, hsa-miR-769-3p, hsa-miR-512-3p, hsa-miR-483-3p, hsa-miR-519d, hsa-miR-1179, hsa-miR-520e, hsa-miR-93, hsa-miR-934, hsa-miR-523, hsa-let-7i, hsa-miR-1292, hsa-miR-520a-3p, hsa-miR-375, hsa-miR-31, hsa-miR-526b, hsa-miR-518c, hsa-miR-519c-3p, hsa-miR-29b-2, hsa-miR-18a, hsa-miR-769-5p, hsa-miR-516-3p, hsa-miR-92a-1, hsa-miR-519a, hsa-miR-519e, hsa-miR-520h, hsa-miR-522, hsa-miR-518f, hsa-miR-148a, hsa-miR-24-2, hsa-miR-524-5p, hsa-miR-29b-1, hsa-miR-516a-5p, hsa-miR-213, hsa-miR-520a-5p, hsa-miR-517, hsa-miR-641, hsa-miR-181a-2, hsa-miR-520f, hsa-miR-151-3p, hsa-miR-373, hsa-miR-944, hsa-miR-371-3p, hsa-miR-518b, hsa-miR-524, hsa-miR-517c, hsa-miR-372, hsa-miR-15b, hsa-miR-151-5P, hsa-miR-520d-5p, hsa-miR-744, hsa-miR-512-5p"]], "row_count": 3, "column_count": 2, "numeric_cells": 4, "header_rows": 1, "locator": "section[23]/table-wrap[2]#db_ds_table-wrap2_reqid_"}}], "gaps": ["asset:data:geo:GSE130489 not downloaded", "asset:data:geo:GSE130489 licence not read", "asset:data:geo:GSE20510 not downloaded", "asset:data:geo:GSE20510 licence not read", "asset:data:geo:GSE32346 not downloaded", "asset:data:geo:GSE32346 licence not read", "asset:data:geo:GSE65654 not downloaded", "asset:data:geo:GSE65654 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The “Limma” package in R software was used to screen out DEmRNAs and DEmiRNAs."}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE20510", "GSE65654", "GSE32346", "GSE130489"], "resolved_accessions": ["GSE20510", "GSE65654", "GSE32346", "GSE130489"], "statements": ["The GSE20510 dataset contained 3 trophoblast samples and 7 CC cell line samples."], "basis": "The paper names GSE20510, GSE65654, GSE32346, GSE130489 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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